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The killings were provoked by a failed coup against then-President Sukarno by a group within the Indonesian armed forces, during which six generals were kidnapped and executed. Suharto and other top commanders quickly quashed the uprising, pinning it on the Indonesian Communist Party.

Security forces and local vigilantes then hunted down people suspected of being communists. An estimated 500,000 people were killed, many of them innocent, and thousands more were locked up without trial.

A large section of the museum is given over to displays justifying the crackdown. Illuminated panels show gory photos of the bodies of the six executed generals, next to a life-size photo of Suharto wearing military fatigues and sunglasses.

There is no mention of the many innocent people killed. Mr. Nugroho, the museum’s director, acknowledged that some killings took place in 1965, but put them down to the spontaneous anger of the Indonesian people.

Baskara T. Wardaya, director of the Center for Democracy and Human Rights Studies at Sanata Dharma University in Yogyakarta, said it was “predictable, and to a certain extent understandable” that a museum built by Suharto’s family would present a one-sided version of history.

But when it comes to the 1965-66 events, he said, the museum mostly reflects the official story that is still told in Indonesian schoolbooks and state museums.

For Mr. Untung, the fact that a monument to Suharto’s legacy could exist while silence prevailed about the killing of thousands of innocents showed that the battle over Indonesia’s history will be drawn-out.

“Suharto is not a legitimate hero,” Mr. Untung said. “If he was a hero, my struggle will be useless.”